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Find kmer locations original sequence #29

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Adamtaranto opened this issue Mar 22, 2023 · 2 comments

Adamtaranto commented Mar 22, 2023

Hi All,

Is it possible to query the bwa index for all locations of a single kmer using prophex?

Member

karel-brinda commented Mar 23, 2023

No, ProphEx doesn't output this. But you can use bwa fastmap (see eg https://github.com/karel-brinda/simplitigs-supplementary/blob/43e09b2052e64eb92fdbea8ee669becb1489ed0e/experiments/multiple_pangenomes_bwa/Snakefile#L54 for how it can be done).

Author

Adamtaranto commented Mar 23, 2023

I was wondering if prophex had an internal method for querying a bwa index that I might be able to re-purpose.

Thanks for the link I'll check out fastmap.

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